2 Answers
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I don't think I've ever heard "protected" as a legal term, at least in this context. Patents are a form of protection, but I definitely wouldn't call them synonymous.

It would help to see an example where "protected" is used in lieu of "patented", but pending that, I'm inclined to say that this is a marketing ploy to make it sound like the invention is patented, when in reality it is not.

Protection is not a formal statutory category, or anything. Well, it's not a category at all, nor a formal concept at all. People refer to "patent protection" as the general sense of protection provided by a patent -- that you get to keep your idea as your own, in some ways, and not have others take it from you, is in some ways a type of security. People talk about "copyright protection" in a similar way. But there is no separate class of intellectual property called "protected stuff," nor any right known as "protection." If somebody tells you their code is "protected," that person might not even mean that there is intellectual property involved -- he might just be saying that he slapped some DRM onto it and you're a big meanie if you try to break it.